org.apache.ctakes.coreference.ae

Class EventCoreferenceAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

org.cleartk.ml.CleartkAnnotator<String>

org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

org.apache.ctakes.coreference.ae.EventCoreferenceAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent, org.apache.uima.fit.factory.initializable.Initializable

@PipeBitInfo(name="Event Coreference Annotator",
             description="Annotates Event Coreferences.",
             dependencies={SECTION,DEPENDENCY_NODE,IDENTIFIED_ANNOTATION,MARKABLE},
             products=COREFERENCE_RELATION)
public class EventCoreferenceAnnotator
extends RelationExtractorAnnotator

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	EventCoreferenceAnnotator.IdentifiedAnnotationPairComparator
class	EventCoreferenceAnnotator.MarkableConfidenceComparator
class	EventCoreferenceAnnotator.MarkablePairConfidenceComparator

Nested classes/interfaces inherited from class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

RelationExtractorAnnotator.IdentifiedAnnotationPair

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_PAR_SIM
static boolean	DEFAULT_SCORE_ALL
static int	DEFAULT_SENT_DIST
protected HashSet<IdentifiedAnnotation>	foundAnaphors
static String	IDENTITY_RELATION
static String	PARAM_PAR_SIM
static String	PARAM_SCORE_ALL
static String	PARAM_SENT_DIST

Fields inherited from class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

category_frequency, coin, NO_RELATION_CATEGORY, PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE, probabilityOfKeepingANegativeExample

Fields inherited from class org.cleartk.ml.CleartkAnnotator

classifier, dataWriter, PARAM_CLASSIFIER_FACTORY_CLASS_NAME, PARAM_DATA_WRITER_FACTORY_CLASS_NAME, PARAM_IS_TRAINING

Constructor Summary

Constructors

Constructor and Description
EventCoreferenceAnnotator()

Method Summary

Modifier and Type	Method and Description
protected String	classify(List<org.cleartk.ml.Feature> features) Predict an outcome given a set of features.
void	collectionProcessComplete()
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription(String modelPath)
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createDataWriterDescription(Class<? extends org.cleartk.ml.DataWriter<String>> dataWriterClass, File outputDirectory, float downsamplingRate)
protected void	createRelation(org.apache.uima.jcas.JCas jCas, IdentifiedAnnotation ante, IdentifiedAnnotation ana, String predictedCategory) Create a UIMA relation type based on arguments and the relation label.
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createScoringAnnotatorDescription(String modelPath)
static boolean	dominates(org.apache.uima.jcas.tcas.Annotation arg1, org.apache.uima.jcas.tcas.Annotation arg2)
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getAlreadyLinkedPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment)
Set<String>	getBestEnt(org.apache.uima.jcas.JCas jcas, Markable markable)
protected Iterable<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getCandidateRelationArgumentPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment) Selects the relevant mentions/annotations within a covering annotation for relation identification/extraction.
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getClosePairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment, double confidence)
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getConfidentPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment, double threshold)
protected Class<? extends org.apache.uima.jcas.tcas.Annotation>	getCoveringClass()
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>>	getFeatureExtractors() Defines the list of feature extractors used by the classifier.
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getHeadwordMatchingPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment)
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getParagraphPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment)
protected String	getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup, IdentifiedAnnotation ante, IdentifiedAnnotation ana) Looks up the arguments in the specified lookup table and converts the relation into a label for classification
protected Class<? extends BinaryTextRelation>	getRelationClass()
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getSectionHeaderPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment, double confidence)
List<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getSimilarPairs(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation segment)
void	process(org.apache.uima.jcas.JCas jCas)
static int	sentDist(org.apache.uima.jcas.JCas jcas, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2)
static int	sentsBetween(IdentifiedAnnotation arg1, IdentifiedAnnotation arg2)

Methods inherited from class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

clearCategoryFrequency, initialize

Methods inherited from class org.cleartk.ml.CleartkAnnotator

isTraining

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

IDENTITY_RELATION

public static final String IDENTITY_RELATION

See Also:

Constant Field Values

DEFAULT_SENT_DIST

public static final int DEFAULT_SENT_DIST

See Also:

Constant Field Values

PARAM_SENT_DIST

public static final String PARAM_SENT_DIST

See Also:

Constant Field Values

DEFAULT_PAR_SIM

public static final double DEFAULT_PAR_SIM

See Also:

Constant Field Values

PARAM_PAR_SIM

public static final String PARAM_PAR_SIM

See Also:

Constant Field Values

DEFAULT_SCORE_ALL

public static final boolean DEFAULT_SCORE_ALL

See Also:

Constant Field Values

PARAM_SCORE_ALL

public static final String PARAM_SCORE_ALL

See Also:

Constant Field Values

foundAnaphors

protected HashSet<IdentifiedAnnotation> foundAnaphors

Constructor Detail

EventCoreferenceAnnotator

public EventCoreferenceAnnotator()

Method Detail

createDataWriterDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createDataWriterDescription(Class<? extends org.cleartk.ml.DataWriter<String>> dataWriterClass,
                                                                                                    File outputDirectory,
                                                                                                    float downsamplingRate)
                                                                                             throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription(String modelPath)
                                                                                            throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException

createScoringAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createScoringAnnotatorDescription(String modelPath)
                                                                                                   throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException

getFeatureExtractors

protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> getFeatureExtractors()

Description copied from class: RelationExtractorAnnotator

Defines the list of feature extractors used by the classifier. Subclasses may override this method to provide a different set of feature extractors.

Overrides:

getFeatureExtractors in class RelationExtractorAnnotator

Returns:

The list of feature extractors to use.

process

public void process(org.apache.uima.jcas.JCas jCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Overrides:

process in class RelationExtractorAnnotator

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

collectionProcessComplete

public void collectionProcessComplete()
                               throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

collectionProcessComplete in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

collectionProcessComplete in class org.cleartk.ml.CleartkAnnotator<String>

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getCandidateRelationArgumentPairs

protected Iterable<RelationExtractorAnnotator.IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(org.apache.uima.jcas.JCas jcas,
                                                                                                          org.apache.uima.jcas.tcas.Annotation segment)

Description copied from class: RelationExtractorAnnotator

Selects the relevant mentions/annotations within a covering annotation for relation identification/extraction.

Specified by:

getCandidateRelationArgumentPairs in class RelationExtractorAnnotator

getClosePairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getClosePairs(org.apache.uima.jcas.JCas jcas,
                                                                               org.apache.uima.jcas.tcas.Annotation segment,
                                                                               double confidence)

getBestEnt

public Set<String> getBestEnt(org.apache.uima.jcas.JCas jcas,
                              Markable markable)

dominates

public static boolean dominates(org.apache.uima.jcas.tcas.Annotation arg1,
                                org.apache.uima.jcas.tcas.Annotation arg2)

getParagraphPairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getParagraphPairs(org.apache.uima.jcas.JCas jcas,
                                                                                   org.apache.uima.jcas.tcas.Annotation segment)

getSimilarPairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getSimilarPairs(org.apache.uima.jcas.JCas jcas,
                                                                                 org.apache.uima.jcas.tcas.Annotation segment)

getConfidentPairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getConfidentPairs(org.apache.uima.jcas.JCas jcas,
                                                                                   org.apache.uima.jcas.tcas.Annotation segment,
                                                                                   double threshold)

getSectionHeaderPairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getSectionHeaderPairs(org.apache.uima.jcas.JCas jcas,
                                                                                       org.apache.uima.jcas.tcas.Annotation segment,
                                                                                       double confidence)

getAlreadyLinkedPairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getAlreadyLinkedPairs(org.apache.uima.jcas.JCas jcas,
                                                                                       org.apache.uima.jcas.tcas.Annotation segment)

getHeadwordMatchingPairs

public List<RelationExtractorAnnotator.IdentifiedAnnotationPair> getHeadwordMatchingPairs(org.apache.uima.jcas.JCas jcas,
                                                                                          org.apache.uima.jcas.tcas.Annotation segment)

classify

protected String classify(List<org.cleartk.ml.Feature> features)
                   throws org.cleartk.ml.CleartkProcessingException

Description copied from class: RelationExtractorAnnotator

Predict an outcome given a set of features. By default, this simply delegates to the object's classifier. Subclasses may override this method to implement more complex classification procedures.

Overrides:

classify in class RelationExtractorAnnotator

Parameters:

features - The features to be classified.

Returns:

The predicted outcome (label) for the features.

Throws:

org.cleartk.ml.CleartkProcessingException

getCoveringClass

protected Class<? extends org.apache.uima.jcas.tcas.Annotation> getCoveringClass()

Specified by:

getCoveringClass in class RelationExtractorAnnotator

getRelationClass

protected Class<? extends BinaryTextRelation> getRelationClass()

Overrides:

getRelationClass in class RelationExtractorAnnotator

createRelation

protected void createRelation(org.apache.uima.jcas.JCas jCas,
                              IdentifiedAnnotation ante,
                              IdentifiedAnnotation ana,
                              String predictedCategory)

Description copied from class: RelationExtractorAnnotator

Create a UIMA relation type based on arguments and the relation label. This allows subclasses to create/define their own types: e.g. coreference can create CoreferenceRelation instead of BinaryTextRelation

Overrides:

createRelation in class RelationExtractorAnnotator

Parameters:

jCas - - JCas object, needed to create new UIMA types

ante - - First argument to relation

ana - - Second argument to relation

predictedCategory - - Name of relation

getRelationCategory

protected String getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
                                     IdentifiedAnnotation ante,
                                     IdentifiedAnnotation ana)

Description copied from class: RelationExtractorAnnotator

Looks up the arguments in the specified lookup table and converts the relation into a label for classification

Overrides:

getRelationCategory in class RelationExtractorAnnotator

Returns:

If this category should not be processed for training return null otherwise it returns the label sent to the datawriter

sentDist

public static int sentDist(org.apache.uima.jcas.JCas jcas,
                           IdentifiedAnnotation arg1,
                           IdentifiedAnnotation arg2)

sentsBetween

public static int sentsBetween(IdentifiedAnnotation arg1,
                               IdentifiedAnnotation arg2)